License: Creative Commons Attribution 4.0 International license (CC BY 4.0)
When quoting this document, please refer to the following
DOI: 10.4230/LIPIcs.DNA.27.7
URN: urn:nbn:de:0030-drops-146749
URL: http://dagstuhl.sunsite.rwth-aachen.de/volltexte/2021/14674/
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Breik, Keenan ; Luchsinger, Austin ; Soloveichik, David

Molecular Machines from Topological Linkages

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LIPIcs-DNA-27-7.pdf (1 MB)

Abstract

Life is built upon amazingly sophisticated molecular machines whose behavior combines mechanical and chemical action. Engineering of similarly complex nanoscale devices from first principles remains an as yet unrealized goal of bioengineering. In this paper we formalize a simple model of mechanical motion (mechanical linkages) combined with chemical bonding. The model has a natural implementation using DNA with double-stranded rigid links, and single-stranded flexible joints and binding sites. Surprisingly, we show that much of the complex behavior is preserved in an idealized topological model which considers solely the graph connectivity of the linkages. We show a number of artifacts including Boolean logic, catalysts, a fueled motor, and chemo-mechanical coupling, all of which can be understood and reasoned about in the topological model. The variety of achieved behaviors supports the use of topological chemical linkages in understanding and engineering complex molecular behaviors.

BibTeX - Entry

@InProceedings{breik_et_al:LIPIcs.DNA.27.7,
  author =	{Breik, Keenan and Luchsinger, Austin and Soloveichik, David},
  title =	{{Molecular Machines from Topological Linkages}},
  booktitle =	{27th International Conference on DNA Computing and Molecular Programming (DNA 27)},
  pages =	{7:1--7:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-205-1},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{205},
  editor =	{Lakin, Matthew R. and \v{S}ulc, Petr},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/opus/volltexte/2021/14674},
  URN =		{urn:nbn:de:0030-drops-146749},
  doi =		{10.4230/LIPIcs.DNA.27.7},
  annote =	{Keywords: chemical computation, mechanical computation, bioengineering, models of biochemistry, molecular machines, mechanical linkages, generic rigidity}
}

Keywords: chemical computation, mechanical computation, bioengineering, models of biochemistry, molecular machines, mechanical linkages, generic rigidity
Collection: 27th International Conference on DNA Computing and Molecular Programming (DNA 27)
Issue Date: 2021
Date of publication: 08.09.2021

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